Journal article
A Deep-Sequencing Workflow for the Fast and Efficient Generation of High-Quality African Swine Fever Virus Whole-Genome Sequences
Friedrich-Loeffler-Institute1
Republican Center for Veterinary Diagnostic2
University of Copenhagen3
Pirbright Institute4
National Veterinary Institute, Technical University of Denmark5
Virology, Division for Diagnostics & Scientific Advice, National Veterinary Institute, Technical University of Denmark6
African swine fever (ASF) is a severe disease of suids caused by African swine fever virus (ASFV). Its dsDNA genome (170-194 kbp) is scattered with homopolymers and repeats as well as inverted-terminal-repeats (ITR), which hamper whole-genome sequencing. To date, only a few genome sequences have been published and only for some are data on sequence quality available enabling in-depth investigations.
Especially in Europe and Asia, where ASFV has continuously spread since its introduction into Georgia in 2007, a very low genetic variability of the circulating ASFV-strains was reported. Therefore, only whole-genome sequences can serve as a basis for detailed virus comparisons. Here, we report an effective workflow, combining target enrichment, Illumina and Nanopore sequencing for ASFV whole-genome sequencing.
Following this approach, we generated an improved high-quality ASFV Georgia 2007/1 whole-genome sequence leading to the correction of 71 sequencing errors and the addition of 956 and 231 bp at the respective ITRs. This genome, derived from the primary outbreak in 2007, can now serve as a reference for future whole-genome analyses of related ASFV strains and molecular approaches.
Using both workflow and the reference genome, we generated the first ASFV-whole-genome sequence from Moldova, expanding the sequence knowledge from Eastern Europe.
Language: | English |
---|---|
Publisher: | MDPI |
Year: | 2019 |
Pages: | 846 |
ISSN: | 19994915 |
Types: | Journal article |
DOI: | 10.3390/v11090846 |
ORCIDs: | Rasmussen, Thomas Bruun , 0000-0001-5319-5436 , 0000-0002-6161-3439 , 0000-0001-8408-2274 , 0000-0002-1286-8590 and 0000-0002-5318-665X |
African Swine Fever African Swine Fever Virus African swine fever virus (ASFV) Animals DNA, Viral Databases, Nucleic Acid Genetic Variation Genome, Viral High-Throughput Nucleotide Sequencing Microbiology Nanopore Sequencing Nanopore sequencing QR1-502 Swine Viral Proteins Whole Genome Sequencing Workflow next-generation sequencing (NGS) target enrichment whole-genome sequencing